Anyway, you have your profile-folder write-protected. If you don't know how to unlock it, and have nothing customized yet, you'd best place your profile into the windows user folder. How:
Delete file "profile.ini" in c://program files/K-Meleon
(your path may vary)
After next browser start you have a new default profile that can store your settings.

Am no expert there, others know more.
Only have read that sometimes people had that problem when using some "cleaning up" program, or special security settings... Then again, have some doubts if in that case KM would produce a new bookmarks_backup each time??

Click Edit > Configuration > Profile directory
that opens the file explorer of your system. Can you check there if your bookmarks.html gets really updated while the browser is open? If it CAN write but gets deleted only after the browser is closed?

Or test what happens if you place it outside the profile folder? In Bookmarks>Options you can choose another path, anywhere else.